Incidental Mutation 'PIT4802001:Virma'
ID 556719
Institutional Source Beutler Lab
Gene Symbol Virma
Ensembl Gene ENSMUSG00000040720
Gene Name vir like m6A methyltransferase associated
Synonyms 1110037F02Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # PIT4802001 (G1)
Quality Score 212.009
Status Not validated
Chromosome 4
Chromosomal Location 11485958-11550684 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 11546008 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Glutamine at position 1615 (H1615Q)
Ref Sequence ENSEMBL: ENSMUSP00000058078 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000059914] [ENSMUST00000108307]
AlphaFold A2AIV2
Predicted Effect probably damaging
Transcript: ENSMUST00000059914
AA Change: H1615Q

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000058078
Gene: ENSMUSG00000040720
AA Change: H1615Q

DomainStartEndE-ValueType
low complexity region 139 153 N/A INTRINSIC
low complexity region 172 198 N/A INTRINSIC
low complexity region 236 267 N/A INTRINSIC
low complexity region 276 297 N/A INTRINSIC
low complexity region 615 625 N/A INTRINSIC
low complexity region 1008 1020 N/A INTRINSIC
low complexity region 1112 1124 N/A INTRINSIC
low complexity region 1224 1232 N/A INTRINSIC
low complexity region 1443 1458 N/A INTRINSIC
low complexity region 1460 1474 N/A INTRINSIC
low complexity region 1618 1634 N/A INTRINSIC
low complexity region 1684 1697 N/A INTRINSIC
low complexity region 1750 1757 N/A INTRINSIC
low complexity region 1796 1808 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000108307
AA Change: H1665Q

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000103943
Gene: ENSMUSG00000040720
AA Change: H1665Q

DomainStartEndE-ValueType
Pfam:VIR_N 5 266 2e-110 PFAM
low complexity region 276 297 N/A INTRINSIC
low complexity region 615 625 N/A INTRINSIC
low complexity region 1058 1070 N/A INTRINSIC
low complexity region 1162 1174 N/A INTRINSIC
low complexity region 1274 1282 N/A INTRINSIC
low complexity region 1493 1508 N/A INTRINSIC
low complexity region 1510 1524 N/A INTRINSIC
low complexity region 1668 1684 N/A INTRINSIC
low complexity region 1734 1747 N/A INTRINSIC
low complexity region 1800 1807 N/A INTRINSIC
low complexity region 1846 1858 N/A INTRINSIC
Coding Region Coverage
  • 1x: 93.6%
  • 3x: 91.0%
  • 10x: 85.4%
  • 20x: 73.7%
Validation Efficiency
Allele List at MGI
Other mutations in this stock
Total: 51 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aatk A T 11: 119,902,172 (GRCm39) D741E probably benign Het
Abca16 A G 7: 120,139,351 (GRCm39) D1461G probably benign Het
Adam6a G T 12: 113,509,078 (GRCm39) D484Y probably damaging Het
Akap5 T C 12: 76,376,706 (GRCm39) Y713H probably damaging Het
AW554918 A G 18: 25,473,132 (GRCm39) E312G possibly damaging Het
Car4 G A 11: 84,855,231 (GRCm39) A157T probably damaging Het
Chst9 A T 18: 15,585,849 (GRCm39) M238K probably benign Het
Ctbp2 G A 7: 132,589,974 (GRCm39) H397Y possibly damaging Het
Cyp3a59 A G 5: 146,039,611 (GRCm39) M295V probably benign Het
Daglb T C 5: 143,488,803 (GRCm39) Y586H probably benign Het
Ehbp1l1 G T 19: 5,769,603 (GRCm39) P567T possibly damaging Het
Emilin2 A G 17: 71,580,464 (GRCm39) I754T probably damaging Het
Esyt2 G A 12: 116,329,457 (GRCm39) A672T probably benign Het
Evx1 G T 6: 52,291,175 (GRCm39) E116* probably null Het
Exph5 T C 9: 53,286,278 (GRCm39) S1120P probably damaging Het
Fam184a A T 10: 53,560,450 (GRCm39) L515* probably null Het
Flt4 T A 11: 49,523,996 (GRCm39) D525E probably benign Het
Galt T C 4: 41,756,764 (GRCm39) W135R probably damaging Het
Ifitm6 A T 7: 140,596,648 (GRCm39) C42S probably damaging Het
Ift172 A G 5: 31,442,610 (GRCm39) S186P probably benign Het
Kcnk3 A G 5: 30,779,712 (GRCm39) E254G probably damaging Het
Kmt2b A G 7: 30,278,996 (GRCm39) S1509P probably damaging Het
Ky T A 9: 102,414,972 (GRCm39) S295T probably benign Het
Lrba T A 3: 86,571,801 (GRCm39) Y2368* probably null Het
Mtmr4 T A 11: 87,501,953 (GRCm39) V669E probably benign Het
Myh10 C T 11: 68,655,918 (GRCm39) R471C probably damaging Het
Nav1 G A 1: 135,380,671 (GRCm39) T1416I unknown Het
Nrip1 A C 16: 76,090,157 (GRCm39) S467A probably damaging Het
Ntrk1 T A 3: 87,695,941 (GRCm39) N190Y probably damaging Het
Or14a256 A T 7: 86,265,763 (GRCm39) L30Q probably null Het
Or5h25 A C 16: 58,930,964 (GRCm39) M3R probably benign Het
Pdxp A G 15: 78,802,611 (GRCm39) S282G probably damaging Het
Phtf2 A T 5: 21,006,904 (GRCm39) S220T probably damaging Het
Piezo2 A T 18: 63,157,540 (GRCm39) V2390E probably damaging Het
Pop1 T G 15: 34,529,229 (GRCm39) L783R probably benign Het
Prf1 G A 10: 61,135,972 (GRCm39) A83T probably benign Het
Rab4b A G 7: 26,875,267 (GRCm39) V50A probably benign Het
Rtn1 T A 12: 72,351,100 (GRCm39) T370S probably benign Het
Sdr16c5 T A 4: 4,012,423 (GRCm39) I123F probably damaging Het
Smg6 T A 11: 75,046,991 (GRCm39) V1228D probably damaging Het
Smim19 A G 8: 22,963,539 (GRCm39) V23A probably benign Het
Sox13 A T 1: 133,313,996 (GRCm39) I346N probably damaging Het
Tap1 T A 17: 34,412,165 (GRCm39) Y457N probably damaging Het
Tbck C T 3: 132,458,427 (GRCm39) P686S probably damaging Het
Tcof1 A G 18: 60,965,010 (GRCm39) S570P unknown Het
Tmc5 A T 7: 118,271,449 (GRCm39) M921L probably benign Het
Ttc6 A G 12: 57,772,462 (GRCm39) Y1594C possibly damaging Het
Vmn1r19 T A 6: 57,382,037 (GRCm39) Y197N probably damaging Het
Vps13c T C 9: 67,845,068 (GRCm39) F2051L probably damaging Het
Wdr6 C T 9: 108,451,765 (GRCm39) C706Y probably damaging Het
Zfand4 A G 6: 116,261,736 (GRCm39) N100D probably damaging Het
Other mutations in Virma
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00428:Virma APN 4 11,519,424 (GRCm39) splice site probably benign
IGL00477:Virma APN 4 11,519,006 (GRCm39) missense probably damaging 0.99
IGL01293:Virma APN 4 11,521,114 (GRCm39) missense probably damaging 1.00
IGL01410:Virma APN 4 11,518,929 (GRCm39) nonsense probably null
IGL01531:Virma APN 4 11,528,753 (GRCm39) missense probably damaging 1.00
IGL01672:Virma APN 4 11,527,792 (GRCm39) missense probably damaging 1.00
IGL01724:Virma APN 4 11,528,672 (GRCm39) missense probably damaging 1.00
IGL01747:Virma APN 4 11,526,877 (GRCm39) missense probably damaging 1.00
IGL01776:Virma APN 4 11,527,792 (GRCm39) missense probably damaging 1.00
IGL02064:Virma APN 4 11,513,163 (GRCm39) missense possibly damaging 0.87
IGL02243:Virma APN 4 11,546,031 (GRCm39) missense probably damaging 1.00
IGL02244:Virma APN 4 11,546,031 (GRCm39) missense probably damaging 1.00
IGL02445:Virma APN 4 11,527,029 (GRCm39) missense probably damaging 0.97
IGL02546:Virma APN 4 11,494,804 (GRCm39) missense probably damaging 0.99
IGL02807:Virma APN 4 11,507,079 (GRCm39) splice site probably benign
IGL02967:Virma APN 4 11,514,096 (GRCm39) missense probably benign 0.01
IGL03211:Virma APN 4 11,548,770 (GRCm39) nonsense probably null
IGL03242:Virma APN 4 11,527,669 (GRCm39) missense possibly damaging 0.70
IGL03256:Virma APN 4 11,542,207 (GRCm39) splice site probably benign
IGL03327:Virma APN 4 11,518,984 (GRCm39) missense probably benign 0.00
IGL03346:Virma APN 4 11,518,984 (GRCm39) missense probably benign 0.00
R0142:Virma UTSW 4 11,548,783 (GRCm39) missense probably benign 0.04
R0355:Virma UTSW 4 11,528,626 (GRCm39) nonsense probably null
R0522:Virma UTSW 4 11,519,416 (GRCm39) critical splice donor site probably null
R0600:Virma UTSW 4 11,498,769 (GRCm39) missense probably damaging 0.99
R1435:Virma UTSW 4 11,528,621 (GRCm39) missense probably damaging 1.00
R1489:Virma UTSW 4 11,521,164 (GRCm39) missense probably damaging 1.00
R1568:Virma UTSW 4 11,528,776 (GRCm39) missense probably damaging 0.99
R1616:Virma UTSW 4 11,544,954 (GRCm39) missense probably damaging 1.00
R1655:Virma UTSW 4 11,494,786 (GRCm39) missense probably damaging 1.00
R1695:Virma UTSW 4 11,494,814 (GRCm39) missense probably damaging 0.98
R1835:Virma UTSW 4 11,540,511 (GRCm39) missense probably benign 0.02
R1951:Virma UTSW 4 11,513,907 (GRCm39) missense probably benign 0.00
R1991:Virma UTSW 4 11,519,242 (GRCm39) missense probably benign 0.06
R2145:Virma UTSW 4 11,548,726 (GRCm39) splice site probably benign
R2172:Virma UTSW 4 11,527,843 (GRCm39) missense possibly damaging 0.82
R2217:Virma UTSW 4 11,544,924 (GRCm39) missense probably damaging 1.00
R2218:Virma UTSW 4 11,544,924 (GRCm39) missense probably damaging 1.00
R2248:Virma UTSW 4 11,518,927 (GRCm39) missense probably damaging 1.00
R2342:Virma UTSW 4 11,501,316 (GRCm39) missense probably damaging 1.00
R3424:Virma UTSW 4 11,513,177 (GRCm39) nonsense probably null
R4397:Virma UTSW 4 11,513,901 (GRCm39) missense possibly damaging 0.81
R4449:Virma UTSW 4 11,498,828 (GRCm39) critical splice donor site probably null
R4660:Virma UTSW 4 11,513,505 (GRCm39) missense probably damaging 1.00
R4698:Virma UTSW 4 11,528,636 (GRCm39) missense probably damaging 0.99
R4878:Virma UTSW 4 11,544,971 (GRCm39) missense probably damaging 1.00
R4937:Virma UTSW 4 11,521,147 (GRCm39) nonsense probably null
R5031:Virma UTSW 4 11,542,116 (GRCm39) nonsense probably null
R5040:Virma UTSW 4 11,528,746 (GRCm39) missense probably benign 0.01
R5061:Virma UTSW 4 11,494,840 (GRCm39) missense possibly damaging 0.95
R5091:Virma UTSW 4 11,519,392 (GRCm39) missense probably benign 0.00
R5137:Virma UTSW 4 11,546,297 (GRCm39) missense probably damaging 1.00
R5262:Virma UTSW 4 11,539,926 (GRCm39) missense probably benign 0.01
R5297:Virma UTSW 4 11,494,819 (GRCm39) missense probably damaging 1.00
R5730:Virma UTSW 4 11,542,154 (GRCm39) missense probably benign 0.44
R5818:Virma UTSW 4 11,513,319 (GRCm39) missense possibly damaging 0.92
R5835:Virma UTSW 4 11,514,036 (GRCm39) missense probably damaging 1.00
R6125:Virma UTSW 4 11,521,172 (GRCm39) missense probably damaging 0.98
R6197:Virma UTSW 4 11,505,498 (GRCm39) missense probably damaging 0.96
R6222:Virma UTSW 4 11,527,820 (GRCm39) missense probably damaging 1.00
R6793:Virma UTSW 4 11,539,968 (GRCm39) missense probably damaging 1.00
R7028:Virma UTSW 4 11,519,249 (GRCm39) missense possibly damaging 0.50
R7356:Virma UTSW 4 11,513,595 (GRCm39) missense probably damaging 0.99
R7383:Virma UTSW 4 11,514,026 (GRCm39) missense probably damaging 0.98
R7391:Virma UTSW 4 11,508,099 (GRCm39) missense probably damaging 0.99
R7425:Virma UTSW 4 11,546,211 (GRCm39) missense possibly damaging 0.95
R7556:Virma UTSW 4 11,518,927 (GRCm39) missense probably damaging 1.00
R7715:Virma UTSW 4 11,513,016 (GRCm39) splice site probably null
R7715:Virma UTSW 4 11,549,682 (GRCm39) missense probably damaging 1.00
R7986:Virma UTSW 4 11,540,023 (GRCm39) missense probably benign 0.01
R7990:Virma UTSW 4 11,513,983 (GRCm39) missense probably benign 0.00
R8048:Virma UTSW 4 11,539,918 (GRCm39) nonsense probably null
R8050:Virma UTSW 4 11,528,643 (GRCm39) missense probably benign 0.22
R8165:Virma UTSW 4 11,542,128 (GRCm39) missense probably benign 0.00
R8412:Virma UTSW 4 11,521,261 (GRCm39) critical splice donor site probably null
R8544:Virma UTSW 4 11,516,949 (GRCm39) missense probably benign
R8551:Virma UTSW 4 11,513,397 (GRCm39) missense probably damaging 1.00
R8699:Virma UTSW 4 11,528,678 (GRCm39) missense probably benign 0.04
R8739:Virma UTSW 4 11,540,643 (GRCm39) critical splice donor site probably null
R8950:Virma UTSW 4 11,519,047 (GRCm39) nonsense probably null
R9015:Virma UTSW 4 11,540,494 (GRCm39) missense probably benign 0.27
R9038:Virma UTSW 4 11,526,922 (GRCm39) missense possibly damaging 0.93
R9115:Virma UTSW 4 11,498,744 (GRCm39) missense probably benign 0.15
R9294:Virma UTSW 4 11,513,507 (GRCm39) nonsense probably null
R9404:Virma UTSW 4 11,513,626 (GRCm39) missense probably benign 0.17
R9477:Virma UTSW 4 11,528,753 (GRCm39) missense probably damaging 1.00
R9532:Virma UTSW 4 11,507,078 (GRCm39) critical splice donor site probably null
R9649:Virma UTSW 4 11,486,045 (GRCm39) start codon destroyed probably null 0.08
R9657:Virma UTSW 4 11,544,898 (GRCm39) missense probably damaging 0.99
R9780:Virma UTSW 4 11,513,442 (GRCm39) missense possibly damaging 0.75
R9800:Virma UTSW 4 11,546,007 (GRCm39) missense probably damaging 0.99
X0020:Virma UTSW 4 11,486,055 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- AGGTGGACGATGACATTTCC -3'
(R):5'- ACGAGAGGAAATCTTTTGTGAGAC -3'

Sequencing Primer
(F):5'- GGACGATGACATTTCCATTGG -3'
(R):5'- AGGAAATCTTTTGTGAGACTTTGAG -3'
Posted On 2019-06-07